256 Hz, and 50% is showing a slow rise/fall.
To be brutally honest, if that's an accurate measurement of light intensity, this is an exceptionally poor PWM performance. I'd be seriously concerned about this.
fuzz around the line -- that's 100 kHz ripple that I'd like to remove.
Do you mean the small-amplitude 'heavy' fuzz (2.5mV amplitude if I read correctly), or the much lighter fuzz that's apparently not there most/some of the time and only sporadically at some points of the period (the 15-20mV amplitude fuzz)? The latter looks like an oscillation; I'd be tempted to scope out the actual current through the LEDs to see if it's there, or if you're picking up a spurious effect in your phototransistor detector circuit.
I think the phototransistor is useful for determining thermal degradation effects, but perhaps less so for measuring PWM performance. To that end, I'd directly measure LED current instead.
If you’re using pwm dimming, a capacitor would cause trouble on low levels at a minimum I think
It would further degrade PWM slope performance, indeed. As such it would affect all duty cycles, with very low ones being erased away and very high ones all glued together to 100%. Depending on component choice / dimensioning, of course. I don't use any caps across the driver outputs for this reason. I do use a much higher PWM frequency; I think I'm running the LEDs at 10kHz now. This used to be 1.5kHz in my previous setup. I'd have to go back to my notes on the buck frequency I chose for the LED drivers, but off the top of my head I set this at 330kHz.